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957
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How to get the refSNP ids or rsIDs of variants from UKbiobank datasets
SNP sequencing genome next-gen
3.6 years ago by a.james ▴ 240
3
votes
4
replies
1.9k
views
Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes
RNA-Seq DNA-seq
updated 12 months ago by ▴ 760 • written 3.8 years ago by ▴ 240
3
votes
1
reply
478
views
how to extact first 100 lines of an indexed BED file
bed genome
4.0 years ago by a.james ▴ 240
0
votes
0
replies
671
views
How to annotate illumina HumanHT-12_V3_0_R3_11283641_A.txt data
genome illumina array
4.0 years ago by a.james ▴ 240
0
votes
2
replies
1.1k
views
Tools for predicting the protein altering effects of the variants from EXON-seq data
Exon-seq variants SNP sequencing
4.2 years ago by a.james ▴ 240
2
votes
1
reply
725
views
Finding the coverage of variants from variant file, which has no DF4 field
assembly RNA-Seq
4.4 years ago by a.james ▴ 240
1
vote
3
replies
1.7k
views
The Picard FilterSAM READ is throwing error
RNA-Seq picard Assembly reads
updated 4.4 years ago by 161k • written 4.4 years ago by ▴ 240
2
votes
3
replies
1.0k
views
Finding the best alignment from a paternal and maternal BAM file
RNA-Seq
updated 4.4 years ago by 8.7k • written 4.4 years ago by ▴ 240
2
votes
4
replies
1.2k
views
Extracting the reads counts (coverage) a specific variant allele from a Fastq file
RNA-Seq snp sequencing
4.5 years ago by a.james ▴ 240
2
votes
4
replies
2.7k
views
How to retrieve metadata from the manifest data and UUID from genomic data commons (GDC)
tcga exon mutations alignment next-gen
4.8 years ago by a.james ▴ 240
3
votes
14
replies
3.6k
views
Where can I download GRCh38-lite.fa file and all_sequences.fa file for hg38 version
exome next-gen alignment
4.8 years ago by a.james ▴ 240
3
votes
2
replies
1.1k
views
CWLtools version problem with usage of secondary files and java expression
CWL
5.0 years ago by a.james ▴ 240
0
votes
0
replies
985
views
How to step dependency in a step based on the output from 2 previous steps in CWL workflow
CW
5.0 years ago by a.james ▴ 240
2
votes
2
replies
2.5k
views
CWL to check the output directory and run for non-existing files
CWL RNA-seq next-gen
5.1 years ago by a.james ▴ 240
0
votes
1
reply
1.7k
views
CWL in toil
CWL Toil
5.1 years ago by a.james ▴ 240
2
votes
2
replies
957
views
CWL for star for multiple bam files with javascript expression
CWL
updated 5.2 years ago by 161k • written 5.2 years ago by ▴ 240
3
votes
4
replies
1.5k
views
CWL to write into for writing lines one from one file to new file
CWL
5.2 years ago by a.james ▴ 240
0
votes
0
replies
1.2k
views
CWL toil-cwl-runner for two samples, could not find a error log and reason for failure
cwl
5.2 years ago by a.james ▴ 240
5
votes
7
replies
2.2k
views
CWL with R returns empty output directory with "Final process status is success" status
CWL RNA-Seq
5.2 years ago by a.james ▴ 240
0
votes
0
replies
2.7k
views
Did not find output file with glob pattern: for creating runtime output directory in CWL
CWL
5.5 years ago by a.james ▴ 240
10
votes
6
replies
4.1k
views
How to calculate the sensitivity and specificity of set of expression dataset used in a validation cohort
gene RNA-Seq
5.5 years ago by a.james ▴ 240
3
votes
5
replies
11k
views
6 follow
MuTect2 VCF file
RNA-Seq SNP VCF
updated 2.8 years ago by ▴ 180 • written 8.2 years ago by ▴ 240
0
votes
7
replies
3.1k
views
Error while parsing vcf file
RNA-Seq sequencing SNP vcf
7.0 years ago by a.james ▴ 240
5
votes
8
replies
2.4k
views
How to get the number of exon within genes from GRCH37 reference
RNA-Seq next-gen gene
updated 7.0 years ago by 161k • written 7.0 years ago by ▴ 240
0
votes
6
replies
3.3k
views
Querying positions (bed file) towards BAM files using samtools mpileup
RNA-Seq
7.2 years ago by a.james ▴ 240
7
votes
15
replies
3.5k
views
GeneSCF gives out more pathways for genes compared to DAVID
RNA-Seq ChIP-Seq GeneSCF
7.8 years ago by a.james ▴ 240
0
votes
7
replies
2.3k
views
How to proceed with SWAN normalized 450k Methyl array data
RNA-Seq next-gen
7.8 years ago by a.james ▴ 240
5
votes
7
replies
5.7k
views
Htseq throws error, No module named pysam,
RNA-Seq ChIP-Seq next-gen sequencing
8.1 years ago by a.james ▴ 240
12
votes
8
replies
6.3k
views
IGV not showing the variants detected by GATK and Varscan
RNA-Seq next-gen-sequencing alignment
updated 20 months ago by 43k • written 8.4 years ago by ▴ 240
4
votes
3
replies
6.7k
views
Minor Allele Frequency calculation from VCF file
RNA-Seq SNP
updated 19 months ago by 43k • written 8.6 years ago by ▴ 240
4
votes
8
replies
2.1k
views
Joint analysis of public RNA-seq samples coming from different extraction protocols
python RNA-Seq sequencing R genome
updated 19 months ago by 43k • written 8.6 years ago by ▴ 240
0
votes
1
reply
1.3k
views
Tools or method to convert SAGE to gene names..
RNA-Seq genome
updated 19 months ago by 43k • written 8.6 years ago by ▴ 240
2
votes
4
replies
3.6k
views
BED file with amplicon information
RNA-Seq SNP next-gen-sequencing
updated 17 months ago by 43k • written 8.8 years ago by ▴ 240
5
votes
3
replies
2.2k
views
Healthy donor RNA-seq samples
RNA-Seq
updated 23 months ago by 43k • written 9.1 years ago by ▴ 240
10
votes
7
replies
9.9k
views
ALL RNA-seq publicly available data
rna-seq
updated 24 months ago by 43k • written 9.2 years ago by ▴ 240
0
votes
0
replies
2.4k
views
How to find the frame shift information from fusion gene sequence
RNA-Seq
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 240
6
votes
9
replies
4.7k
views
Pathway Graphs for gene set from RNA-seq
RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 240
3
votes
2
replies
3.9k
views
DESeq output from RNA-seq
sequencing rna-seq next-gen
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 240
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